def score_and_link_cycles(args):
if args.binwidth:
histseg.Global_BINWIDTH = args.binwidth
if not args.historystats and args.cnavg:
historyScores = histseg.combine_history_statsfiles(args.cnavg)
elif not os.path.isfile(args.historystats) and args.cnavg:
historyScores = histseg.combine_history_statsfiles(args.cnavg)
np.savetxt(args.historystats, historyScores, fmt="%d", delimiter='\t')
elif os.path.isfile(args.historystats):
historyScores = np.loadtxt(args.historystats, dtype=int)
if not historyScores:
sys.exit("Need to use --historystats or --cnavg option")
totalp = 0
if args.totalp:
totalp = args.totalp
else:
totalp = histseg.compute_likelihood_histories(historyScores[:, 0],
historyScores)
allevents = []
if args.cnavg:
sys.stderr.write("using cnavg dir: %s\n" % (args.cnavg))
allevents = histseg.get_events_from_cnavgdir(args.cnavg, historyScores,
totalp)
elif args.inpickle and os.path.isfile(args.inpickle):
sys.stderr.write("using pickle file\n")
allevents = pickle.load(open(args.inpickle, 'rb'))
sys.stderr.write("there are %d events\n" % (len(allevents)))
if args.outpickle:
for event in allevents:
event.trim()
eventfile = open(args.outpickle, 'wb')
pickle.dump(allevents, eventfile, pickle.HIGHEST_PROTOCOL)
if args.events:
eventfile = open(args.events, 'w')
for evnt in allevents:
eventfile.write("%s" % (str(evnt)))
# link the events...
if args.links:
if not allevents:
sys.exit(
"Need events to link! use --inpickle or --cnavg or --events")
if not totalp:
sys.exit("Need a --totalp or --cnavg or --historystats options")
eventlinks = link_events_by_order_within_histories(allevents)
linkfile = open(args.links, 'w')
for link in eventlinks:
link.likelihood = histseg.compute_likelihood_histories(
link.histories, historyScores)
linkfile.write("%s" % (str(link)))
def score_and_link_cycles(args):
if args.binwidth:
histseg.Global_BINWIDTH=args.binwidth
if not args.historystats and args.cnavg:
historyScores=histseg.combine_history_statsfiles(args.cnavg)
elif not os.path.isfile(args.historystats) and args.cnavg:
historyScores=histseg.combine_history_statsfiles(args.cnavg)
np.savetxt(args.historystats, historyScores, fmt="%d", delimiter='\t')
elif os.path.isfile(args.historystats):
historyScores=np.loadtxt(args.historystats, dtype=int)
if not historyScores:
sys.exit("Need to use --historystats or --cnavg option")
totalp=0
if args.totalp:
totalp=args.totalp
else:
totalp = histseg.compute_likelihood_histories(historyScores[:,0], historyScores)
allevents=[]
if args.cnavg:
sys.stderr.write("using cnavg dir: %s\n" % (args.cnavg))
allevents=histseg.get_events_from_cnavgdir(args.cnavg, historyScores, totalp)
elif args.inpickle and os.path.isfile(args.inpickle):
sys.stderr.write("using pickle file\n")
allevents=pickle.load(open(args.inpickle, 'rb'))
sys.stderr.write("there are %d events\n" % (len(allevents)))
if args.outpickle:
for event in allevents:
event.trim()
eventfile= open(args.outpickle, 'wb')
pickle.dump(allevents, eventfile, pickle.HIGHEST_PROTOCOL)
if args.events:
eventfile=open(args.events, 'w')
for evnt in allevents:
eventfile.write("%s" % (str(evnt)))
# link the events...
if args.links:
if not allevents:
sys.exit("Need events to link! use --inpickle or --cnavg or --events")
if not totalp:
sys.exit("Need a --totalp or --cnavg or --historystats options")
eventlinks = link_events_by_order_within_histories(allevents)
linkfile=open(args.links, 'w')
for link in eventlinks:
link.likelihood=histseg.compute_likelihood_histories(link.histories, historyScores)
linkfile.write("%s" % (str(link)))
def run(self):
opts=self.options
if opts.simulation:
truefile=os.path.join(opts.cnavgout, "true.braney")
truehist=os.path.join(opts.cnavgout, "HISTORIES_0.braney")
# subprocess.call("grep -v ^$ %s | gzip > %s" % (truefile, truehist), shell=True)
subprocess.check_call("awk 'BEGIN{OFS=\"\\t\"}{if ($1==\"A\" && $9>1) $9=1; if($1 != \"A\" && $5>1) $5=1; print $0}' %s | sed 1d | gzip > %s" % (truefile, truehist), shell=True)
make_STATS_from_truebraney(truefile, os.path.join(opts.cnavgout, "HISTORY_STATS_0"))
statsfiles=glob.glob(self.cnavgout+"/"+"HISTORY_STATS*")
sys.stderr.write("statsfiles: %s\n" % (str(statsfiles)))
historyScores=histseg.combine_history_statsfiles(self.cnavgout)
np.savetxt(self.historystatsfile, historyScores, fmt='%d', delimiter='\t')
def run(self):
opts = self.options
if opts.simulation:
truefile = os.path.join(opts.cnavgout, "true.braney")
truehist = os.path.join(opts.cnavgout, "HISTORIES_0.braney")
# subprocess.call("grep -v ^$ %s | gzip > %s" % (truefile, truehist), shell=True)
subprocess.check_call(
"awk 'BEGIN{OFS=\"\\t\"}{if ($1==\"A\" && $9>1) $9=1; if($1 != \"A\" && $5>1) $5=1; print $0}' %s | sed 1d | gzip > %s"
% (truefile, truehist),
shell=True)
make_STATS_from_truebraney(
truefile, os.path.join(opts.cnavgout, "HISTORY_STATS_0"))
statsfiles = glob.glob(self.cnavgout + "/" + "HISTORY_STATS*")
sys.stderr.write("statsfiles: %s\n" % (str(statsfiles)))
historyScores = histseg.combine_history_statsfiles(self.cnavgout)
np.savetxt(self.historystatsfile,
historyScores,
fmt='%d',
delimiter='\t')
